Starting phenix.real_space_refine on Thu Jul 31 14:58:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4k_41034/07_2025/8t4k_41034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4k_41034/07_2025/8t4k_41034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4k_41034/07_2025/8t4k_41034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4k_41034/07_2025/8t4k_41034.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4k_41034/07_2025/8t4k_41034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4k_41034/07_2025/8t4k_41034.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8562 2.51 5 N 2310 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13560 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3396 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain breaks: 5 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: I, H, E, F, C, D Time building chain proxies: 10.05, per 1000 atoms: 0.74 Number of scatterers: 13560 At special positions: 0 Unit cell: (121.027, 123.431, 116.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2583 8.00 N 2310 7.00 C 8562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 386 " " NAG A 611 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 301 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 386 " " NAG C 611 " - " ASN C 448 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 234 " " NAG D 606 " - " ASN D 276 " " NAG D 607 " - " ASN D 295 " " NAG D 608 " - " ASN D 301 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 386 " " NAG D 611 " - " ASN D 448 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN C 262 " " NAG I 1 " - " ASN D 262 " Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 28.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.048A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.529A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.048A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.530A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.049A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 3.906A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.437A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.570A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.529A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.567A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.567A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN C 301 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AB6, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.209A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.566A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 312 removed outlier: 6.890A pdb=" N ASN D 301 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 315 through 323A current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 459 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4293 1.35 - 1.47: 3440 1.47 - 1.60: 5959 1.60 - 1.72: 0 1.72 - 1.85: 144 Bond restraints: 13836 Sorted by residual: bond pdb=" N GLU C 269 " pdb=" CA GLU C 269 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.29e-02 6.01e+03 9.97e+00 bond pdb=" N VAL D 270 " pdb=" CA VAL D 270 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" N VAL C 270 " pdb=" CA VAL C 270 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.30e-02 5.92e+03 9.89e+00 bond pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta sigma weight residual 1.456 1.496 -0.041 1.30e-02 5.92e+03 9.77e+00 bond pdb=" N GLU A 269 " pdb=" CA GLU A 269 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.65e+00 ... (remaining 13831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 16825 1.71 - 3.43: 1625 3.43 - 5.14: 249 5.14 - 6.85: 48 6.85 - 8.56: 12 Bond angle restraints: 18759 Sorted by residual: angle pdb=" CA PRO A 240 " pdb=" N PRO A 240 " pdb=" CD PRO A 240 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" CA PRO D 240 " pdb=" N PRO D 240 " pdb=" CD PRO D 240 " ideal model delta sigma weight residual 112.00 104.43 7.57 1.40e+00 5.10e-01 2.93e+01 angle pdb=" CA PRO C 240 " pdb=" N PRO C 240 " pdb=" CD PRO C 240 " ideal model delta sigma weight residual 112.00 104.45 7.55 1.40e+00 5.10e-01 2.91e+01 angle pdb=" N GLN D 246 " pdb=" CA GLN D 246 " pdb=" C GLN D 246 " ideal model delta sigma weight residual 113.88 107.48 6.40 1.23e+00 6.61e-01 2.71e+01 angle pdb=" N GLN A 246 " pdb=" CA GLN A 246 " pdb=" C GLN A 246 " ideal model delta sigma weight residual 113.88 107.50 6.38 1.23e+00 6.61e-01 2.69e+01 ... (remaining 18754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8217 17.71 - 35.42: 405 35.42 - 53.13: 153 53.13 - 70.84: 42 70.84 - 88.56: 24 Dihedral angle restraints: 8841 sinusoidal: 4107 harmonic: 4734 Sorted by residual: dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.22 50.22 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.20 50.20 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.19 50.19 1 1.00e+01 1.00e-02 3.45e+01 ... (remaining 8838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1960 0.108 - 0.216: 254 0.216 - 0.323: 3 0.323 - 0.431: 0 0.431 - 0.539: 3 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CB ILE F 595 " pdb=" CA ILE F 595 " pdb=" CG1 ILE F 595 " pdb=" CG2 ILE F 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.27e+00 chirality pdb=" CB ILE E 595 " pdb=" CA ILE E 595 " pdb=" CG1 ILE E 595 " pdb=" CG2 ILE E 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" CB ILE B 595 " pdb=" CA ILE B 595 " pdb=" CG1 ILE B 595 " pdb=" CG2 ILE B 595 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 2217 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 639 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C THR F 639 " -0.074 2.00e-02 2.50e+03 pdb=" O THR F 639 " 0.028 2.00e-02 2.50e+03 pdb=" N GLN F 640 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 639 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C THR E 639 " 0.073 2.00e-02 2.50e+03 pdb=" O THR E 639 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN E 640 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 639 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C THR B 639 " 0.073 2.00e-02 2.50e+03 pdb=" O THR B 639 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN B 640 " -0.025 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 9 2.00 - 2.73: 780 2.73 - 3.45: 17621 3.45 - 4.18: 35084 4.18 - 4.90: 58772 Nonbonded interactions: 112266 Sorted by model distance: nonbonded pdb=" NZ LYS B 655 " pdb=" SD MET E 535 " model vdw 1.281 3.480 nonbonded pdb=" NZ LYS E 655 " pdb=" SD MET F 535 " model vdw 1.281 3.480 nonbonded pdb=" SD MET B 535 " pdb=" NZ LYS F 655 " model vdw 1.282 3.480 nonbonded pdb=" CE LYS B 655 " pdb=" SD MET E 535 " model vdw 1.447 3.800 nonbonded pdb=" SD MET B 535 " pdb=" CE LYS F 655 " model vdw 1.447 3.800 ... (remaining 112261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 208.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 34.270 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 13908 Z= 0.327 Angle : 1.124 8.565 18942 Z= 0.636 Chirality : 0.067 0.539 2220 Planarity : 0.008 0.078 2316 Dihedral : 13.194 88.556 5670 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.87 % Rotamer: Outliers : 0.62 % Allowed : 7.22 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1590 helix: 0.19 (0.24), residues: 414 sheet: 0.72 (0.22), residues: 462 loop : 1.14 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C 479 HIS 0.033 0.004 HIS C 66 PHE 0.022 0.003 PHE A 383 TYR 0.012 0.003 TYR E 643 ARG 0.014 0.002 ARG C 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 36) link_NAG-ASN : angle 2.90803 ( 108) link_BETA1-4 : bond 0.00228 ( 3) link_BETA1-4 : angle 2.97889 ( 9) hydrogen bonds : bond 0.15784 ( 459) hydrogen bonds : angle 7.48111 ( 1251) SS BOND : bond 0.00580 ( 33) SS BOND : angle 2.25159 ( 66) covalent geometry : bond 0.00717 (13836) covalent geometry : angle 1.09735 (18759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.9001 (mmp) cc_final: 0.8733 (mpp) REVERT: B 588 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7665 (ttp-110) REVERT: C 325 HIS cc_start: 0.7525 (m90) cc_final: 0.7130 (m90) REVERT: C 419 TRP cc_start: 0.8225 (m-90) cc_final: 0.7796 (m100) REVERT: E 588 ARG cc_start: 0.7837 (ttp-110) cc_final: 0.7441 (ttp-110) REVERT: D 166 ARG cc_start: 0.8043 (ttp80) cc_final: 0.6570 (mmt90) REVERT: D 327 ARG cc_start: 0.7529 (mtm180) cc_final: 0.7224 (mmt180) REVERT: F 588 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7706 (ttp-110) outliers start: 9 outliers final: 0 residues processed: 219 average time/residue: 1.5340 time to fit residues: 363.5509 Evaluate side-chains 189 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 607 ASN B 653 GLN C 66 HIS C 352 HIS E 591 GLN ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118402 restraints weight = 13851.277| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.65 r_work: 0.3167 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 13908 Z= 0.241 Angle : 0.729 10.804 18942 Z= 0.378 Chirality : 0.051 0.185 2220 Planarity : 0.005 0.047 2316 Dihedral : 5.458 22.838 2553 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.89 % Allowed : 7.97 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1590 helix: 1.35 (0.27), residues: 417 sheet: 0.69 (0.22), residues: 456 loop : 0.64 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 479 HIS 0.008 0.001 HIS C 66 PHE 0.015 0.003 PHE D 383 TYR 0.013 0.002 TYR D 384 ARG 0.005 0.001 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 36) link_NAG-ASN : angle 2.45404 ( 108) link_BETA1-4 : bond 0.00232 ( 3) link_BETA1-4 : angle 1.83514 ( 9) hydrogen bonds : bond 0.06967 ( 459) hydrogen bonds : angle 5.39225 ( 1251) SS BOND : bond 0.00841 ( 33) SS BOND : angle 1.93008 ( 66) covalent geometry : bond 0.00578 (13836) covalent geometry : angle 0.69780 (18759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7641 (mmt90) REVERT: B 633 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6532 (mtpt) REVERT: C 178 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8321 (ptt90) REVERT: C 347 LYS cc_start: 0.7659 (pttp) cc_final: 0.7400 (pptt) REVERT: C 500 ARG cc_start: 0.8009 (mmt180) cc_final: 0.7598 (mmt90) REVERT: E 588 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7828 (ttp-110) REVERT: D 54 CYS cc_start: 0.7341 (t) cc_final: 0.6979 (t) REVERT: D 500 ARG cc_start: 0.7868 (mmt180) cc_final: 0.7357 (mmt90) REVERT: F 601 LYS cc_start: 0.7363 (mptt) cc_final: 0.7162 (mmmm) REVERT: F 633 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6420 (mtpt) outliers start: 42 outliers final: 15 residues processed: 221 average time/residue: 1.3542 time to fit residues: 325.1671 Evaluate side-chains 205 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 352 HIS E 591 GLN E 640 GLN D 352 HIS ** F 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 640 GLN F 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.147773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118404 restraints weight = 14036.697| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.69 r_work: 0.3175 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13908 Z= 0.183 Angle : 0.640 12.915 18942 Z= 0.327 Chirality : 0.047 0.174 2220 Planarity : 0.004 0.038 2316 Dihedral : 5.358 23.837 2553 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.37 % Allowed : 9.07 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1590 helix: 1.49 (0.27), residues: 420 sheet: 0.83 (0.22), residues: 456 loop : 0.34 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 479 HIS 0.004 0.001 HIS D 352 PHE 0.013 0.002 PHE C 383 TYR 0.012 0.002 TYR A 217 ARG 0.002 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 36) link_NAG-ASN : angle 2.29817 ( 108) link_BETA1-4 : bond 0.00165 ( 3) link_BETA1-4 : angle 1.61858 ( 9) hydrogen bonds : bond 0.05673 ( 459) hydrogen bonds : angle 5.13153 ( 1251) SS BOND : bond 0.00609 ( 33) SS BOND : angle 1.83970 ( 66) covalent geometry : bond 0.00440 (13836) covalent geometry : angle 0.60821 (18759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7385 (t) cc_final: 0.7002 (t) REVERT: A 268 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.7005 (pt0) REVERT: A 328 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8595 (tpt) REVERT: A 500 ARG cc_start: 0.8023 (mmt180) cc_final: 0.7537 (mtt-85) REVERT: B 601 LYS cc_start: 0.7575 (mptt) cc_final: 0.7353 (mtpt) REVERT: B 633 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6478 (mtpt) REVERT: B 661 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6807 (mp) REVERT: C 347 LYS cc_start: 0.7698 (pttp) cc_final: 0.7400 (pptt) REVERT: C 500 ARG cc_start: 0.7998 (mmt180) cc_final: 0.7596 (mtt-85) REVERT: E 535 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7940 (mmm) REVERT: E 588 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7702 (ttp-110) REVERT: D 54 CYS cc_start: 0.7331 (t) cc_final: 0.7004 (t) REVERT: D 166 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8132 (ttp80) REVERT: D 268 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6781 (pt0) REVERT: D 500 ARG cc_start: 0.7875 (mmt180) cc_final: 0.7348 (mtt-85) REVERT: F 601 LYS cc_start: 0.7456 (mptt) cc_final: 0.7252 (mtmt) REVERT: F 633 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6398 (mtpt) outliers start: 49 outliers final: 17 residues processed: 211 average time/residue: 1.4042 time to fit residues: 321.2390 Evaluate side-chains 200 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** E 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN D 352 HIS F 585 HIS F 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.148959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119650 restraints weight = 13923.111| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.67 r_work: 0.3195 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13908 Z= 0.143 Angle : 0.593 14.015 18942 Z= 0.300 Chirality : 0.045 0.161 2220 Planarity : 0.004 0.037 2316 Dihedral : 5.100 24.240 2553 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.09 % Allowed : 10.24 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1590 helix: 1.65 (0.27), residues: 420 sheet: 1.12 (0.23), residues: 432 loop : 0.27 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 479 HIS 0.003 0.001 HIS D 352 PHE 0.010 0.002 PHE A 391 TYR 0.014 0.001 TYR A 217 ARG 0.003 0.000 ARG C 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 36) link_NAG-ASN : angle 2.13729 ( 108) link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 1.49249 ( 9) hydrogen bonds : bond 0.04972 ( 459) hydrogen bonds : angle 4.97281 ( 1251) SS BOND : bond 0.00554 ( 33) SS BOND : angle 1.63916 ( 66) covalent geometry : bond 0.00338 (13836) covalent geometry : angle 0.56397 (18759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7277 (t) cc_final: 0.6937 (t) REVERT: A 328 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8526 (tpt) REVERT: A 430 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 500 ARG cc_start: 0.8035 (mmt180) cc_final: 0.7584 (mtt-85) REVERT: C 54 CYS cc_start: 0.7284 (t) cc_final: 0.6941 (t) REVERT: C 103 GLN cc_start: 0.8291 (mt0) cc_final: 0.7265 (tm-30) REVERT: C 137 LYS cc_start: 0.7606 (mttt) cc_final: 0.6555 (pmtt) REVERT: C 347 LYS cc_start: 0.7693 (pttp) cc_final: 0.7372 (pptt) REVERT: C 500 ARG cc_start: 0.7955 (mmt180) cc_final: 0.7648 (mtt-85) REVERT: E 535 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7950 (mmm) REVERT: D 54 CYS cc_start: 0.7241 (t) cc_final: 0.6957 (t) REVERT: D 500 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7407 (mtt-85) outliers start: 45 outliers final: 18 residues processed: 205 average time/residue: 1.4034 time to fit residues: 312.5352 Evaluate side-chains 195 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN D 352 HIS F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120563 restraints weight = 14130.061| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.68 r_work: 0.3206 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13908 Z= 0.128 Angle : 0.573 13.591 18942 Z= 0.287 Chirality : 0.045 0.158 2220 Planarity : 0.003 0.033 2316 Dihedral : 4.935 24.158 2553 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.23 % Allowed : 10.10 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1590 helix: 1.76 (0.27), residues: 420 sheet: 0.99 (0.23), residues: 444 loop : 0.29 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 479 HIS 0.003 0.001 HIS D 105 PHE 0.009 0.001 PHE C 383 TYR 0.011 0.001 TYR A 217 ARG 0.002 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 36) link_NAG-ASN : angle 2.04304 ( 108) link_BETA1-4 : bond 0.00273 ( 3) link_BETA1-4 : angle 1.43346 ( 9) hydrogen bonds : bond 0.04672 ( 459) hydrogen bonds : angle 4.83251 ( 1251) SS BOND : bond 0.00532 ( 33) SS BOND : angle 1.44998 ( 66) covalent geometry : bond 0.00302 (13836) covalent geometry : angle 0.54720 (18759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7238 (t) cc_final: 0.6923 (t) REVERT: A 137 LYS cc_start: 0.7556 (mttt) cc_final: 0.6559 (pmtt) REVERT: A 328 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8581 (tpt) REVERT: A 430 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7941 (mp) REVERT: A 500 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7513 (mmt90) REVERT: B 633 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6430 (mtpt) REVERT: B 657 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7016 (tp30) REVERT: C 103 GLN cc_start: 0.8286 (mt0) cc_final: 0.7258 (tm-30) REVERT: C 137 LYS cc_start: 0.7622 (mttt) cc_final: 0.6586 (pmtt) REVERT: C 325 HIS cc_start: 0.7983 (m-70) cc_final: 0.7554 (m170) REVERT: C 328 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8565 (tpt) REVERT: C 347 LYS cc_start: 0.7649 (pttp) cc_final: 0.7314 (pptt) REVERT: C 500 ARG cc_start: 0.7966 (mmt180) cc_final: 0.7657 (mtt-85) REVERT: E 535 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7958 (mmm) REVERT: D 54 CYS cc_start: 0.7188 (t) cc_final: 0.6905 (t) REVERT: D 114 GLN cc_start: 0.7756 (mt0) cc_final: 0.7404 (pt0) REVERT: D 347 LYS cc_start: 0.7606 (pttp) cc_final: 0.7289 (pptt) REVERT: D 500 ARG cc_start: 0.7938 (mmt180) cc_final: 0.7484 (mmt90) outliers start: 47 outliers final: 19 residues processed: 205 average time/residue: 1.4870 time to fit residues: 330.8222 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 154 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 69 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN F 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.149239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120292 restraints weight = 14172.508| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.68 r_work: 0.3189 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13908 Z= 0.138 Angle : 0.587 13.066 18942 Z= 0.293 Chirality : 0.045 0.167 2220 Planarity : 0.004 0.035 2316 Dihedral : 4.940 23.844 2553 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.23 % Allowed : 10.38 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1590 helix: 1.75 (0.27), residues: 420 sheet: 0.97 (0.23), residues: 438 loop : 0.24 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 479 HIS 0.002 0.001 HIS C 105 PHE 0.010 0.001 PHE A 383 TYR 0.010 0.001 TYR A 217 ARG 0.003 0.000 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 36) link_NAG-ASN : angle 2.07447 ( 108) link_BETA1-4 : bond 0.00216 ( 3) link_BETA1-4 : angle 1.46441 ( 9) hydrogen bonds : bond 0.04745 ( 459) hydrogen bonds : angle 4.82663 ( 1251) SS BOND : bond 0.00529 ( 33) SS BOND : angle 1.51375 ( 66) covalent geometry : bond 0.00324 (13836) covalent geometry : angle 0.55996 (18759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7235 (t) cc_final: 0.6928 (t) REVERT: A 328 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8598 (tpt) REVERT: A 430 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 500 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7523 (mmt90) REVERT: B 633 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6481 (mtpt) REVERT: B 657 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: B 661 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6613 (mp) REVERT: C 103 GLN cc_start: 0.8299 (mt0) cc_final: 0.7256 (tm-30) REVERT: C 114 GLN cc_start: 0.7655 (mt0) cc_final: 0.7402 (pt0) REVERT: C 137 LYS cc_start: 0.7605 (mttt) cc_final: 0.6543 (pmtt) REVERT: C 325 HIS cc_start: 0.7925 (m-70) cc_final: 0.7524 (m170) REVERT: C 328 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8556 (tpt) REVERT: C 347 LYS cc_start: 0.7621 (pttp) cc_final: 0.7285 (pptt) REVERT: C 500 ARG cc_start: 0.7974 (mmt180) cc_final: 0.7665 (mtt-85) REVERT: E 535 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7969 (mmm) REVERT: D 54 CYS cc_start: 0.7202 (t) cc_final: 0.6924 (t) REVERT: D 114 GLN cc_start: 0.7767 (mt0) cc_final: 0.7398 (pt0) REVERT: D 166 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7287 (ttp80) REVERT: D 347 LYS cc_start: 0.7612 (pttp) cc_final: 0.7280 (pptt) REVERT: D 500 ARG cc_start: 0.7951 (mmt180) cc_final: 0.7503 (mmt90) REVERT: F 633 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6421 (mtpt) REVERT: F 657 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7170 (tp30) outliers start: 47 outliers final: 19 residues processed: 200 average time/residue: 1.4805 time to fit residues: 319.6270 Evaluate side-chains 195 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 127 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124311 restraints weight = 14278.084| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.51 r_work: 0.3274 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13908 Z= 0.145 Angle : 0.592 12.641 18942 Z= 0.296 Chirality : 0.046 0.173 2220 Planarity : 0.004 0.034 2316 Dihedral : 4.994 23.716 2553 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.96 % Allowed : 10.93 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1590 helix: 1.82 (0.27), residues: 417 sheet: 0.93 (0.23), residues: 438 loop : 0.24 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 479 HIS 0.002 0.001 HIS C 105 PHE 0.010 0.001 PHE D 383 TYR 0.010 0.001 TYR A 217 ARG 0.003 0.000 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 36) link_NAG-ASN : angle 2.10832 ( 108) link_BETA1-4 : bond 0.00143 ( 3) link_BETA1-4 : angle 1.49694 ( 9) hydrogen bonds : bond 0.04830 ( 459) hydrogen bonds : angle 4.81807 ( 1251) SS BOND : bond 0.00560 ( 33) SS BOND : angle 1.51682 ( 66) covalent geometry : bond 0.00343 (13836) covalent geometry : angle 0.56527 (18759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7292 (t) cc_final: 0.7021 (t) REVERT: A 151 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8402 (ttm170) REVERT: A 500 ARG cc_start: 0.8032 (mmt180) cc_final: 0.7581 (mtt-85) REVERT: B 633 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6446 (mtpt) REVERT: C 103 GLN cc_start: 0.8363 (mt0) cc_final: 0.7377 (tm-30) REVERT: C 114 GLN cc_start: 0.7736 (mt0) cc_final: 0.7510 (pt0) REVERT: C 137 LYS cc_start: 0.7748 (mttt) cc_final: 0.6724 (pmtt) REVERT: C 325 HIS cc_start: 0.7884 (m-70) cc_final: 0.7463 (m170) REVERT: C 328 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8511 (tpt) REVERT: C 347 LYS cc_start: 0.7678 (pttp) cc_final: 0.7355 (pptt) REVERT: C 500 ARG cc_start: 0.7955 (mmt180) cc_final: 0.7647 (mtt-85) REVERT: E 535 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: D 54 CYS cc_start: 0.7213 (t) cc_final: 0.6955 (t) REVERT: D 114 GLN cc_start: 0.7776 (mt0) cc_final: 0.7471 (pt0) REVERT: D 166 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7265 (ttp80) REVERT: D 327 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7568 (mmt180) REVERT: D 347 LYS cc_start: 0.7617 (pttp) cc_final: 0.7303 (pptt) REVERT: D 500 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7518 (mmt90) REVERT: F 633 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6434 (mtpt) outliers start: 43 outliers final: 19 residues processed: 195 average time/residue: 1.4416 time to fit residues: 304.5684 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124685 restraints weight = 14181.747| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.61 r_work: 0.3267 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13908 Z= 0.140 Angle : 0.585 12.175 18942 Z= 0.292 Chirality : 0.046 0.170 2220 Planarity : 0.004 0.035 2316 Dihedral : 4.989 23.881 2553 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.68 % Allowed : 11.62 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1590 helix: 1.83 (0.27), residues: 417 sheet: 0.95 (0.23), residues: 438 loop : 0.23 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 419 HIS 0.002 0.001 HIS C 105 PHE 0.010 0.001 PHE D 383 TYR 0.011 0.001 TYR A 217 ARG 0.004 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 36) link_NAG-ASN : angle 2.09025 ( 108) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.47881 ( 9) hydrogen bonds : bond 0.04738 ( 459) hydrogen bonds : angle 4.78752 ( 1251) SS BOND : bond 0.00544 ( 33) SS BOND : angle 1.44409 ( 66) covalent geometry : bond 0.00332 (13836) covalent geometry : angle 0.55861 (18759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7344 (t) cc_final: 0.7080 (t) REVERT: A 141 MET cc_start: 0.7830 (ttm) cc_final: 0.7623 (ttt) REVERT: A 328 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8617 (tpt) REVERT: A 430 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7893 (mp) REVERT: A 500 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7569 (mtt-85) REVERT: B 633 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6506 (mtpt) REVERT: C 114 GLN cc_start: 0.7721 (mt0) cc_final: 0.7517 (pt0) REVERT: C 137 LYS cc_start: 0.7809 (mttt) cc_final: 0.6764 (pmtt) REVERT: C 325 HIS cc_start: 0.7888 (m-70) cc_final: 0.7495 (m170) REVERT: C 328 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8565 (tpt) REVERT: C 347 LYS cc_start: 0.7672 (pttp) cc_final: 0.7344 (pptt) REVERT: C 500 ARG cc_start: 0.7968 (mmt180) cc_final: 0.7645 (mtt-85) REVERT: E 535 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: E 588 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7867 (ttp-110) REVERT: D 54 CYS cc_start: 0.7195 (t) cc_final: 0.6940 (t) REVERT: D 114 GLN cc_start: 0.7808 (mt0) cc_final: 0.7538 (pt0) REVERT: D 166 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7275 (ttp80) REVERT: D 327 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7600 (mmt180) REVERT: D 347 LYS cc_start: 0.7623 (pttp) cc_final: 0.7303 (pptt) REVERT: D 500 ARG cc_start: 0.7866 (mmt180) cc_final: 0.7463 (mmt90) REVERT: F 657 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7229 (tp30) outliers start: 39 outliers final: 21 residues processed: 189 average time/residue: 1.4587 time to fit residues: 298.4596 Evaluate side-chains 195 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 145 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 591 GLN E 591 GLN E 651 ASN F 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119597 restraints weight = 14188.173| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.58 r_work: 0.3198 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 13908 Z= 0.322 Angle : 0.801 16.258 18942 Z= 0.397 Chirality : 0.054 0.214 2220 Planarity : 0.005 0.044 2316 Dihedral : 5.965 29.186 2553 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.61 % Allowed : 11.89 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1590 helix: 1.27 (0.26), residues: 417 sheet: 0.94 (0.24), residues: 384 loop : -0.03 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 69 HIS 0.005 0.001 HIS A 249 PHE 0.016 0.002 PHE C 383 TYR 0.016 0.003 TYR A 384 ARG 0.004 0.001 ARG C 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 36) link_NAG-ASN : angle 2.72917 ( 108) link_BETA1-4 : bond 0.00167 ( 3) link_BETA1-4 : angle 1.98575 ( 9) hydrogen bonds : bond 0.06687 ( 459) hydrogen bonds : angle 5.37113 ( 1251) SS BOND : bond 0.00876 ( 33) SS BOND : angle 2.16951 ( 66) covalent geometry : bond 0.00779 (13836) covalent geometry : angle 0.76619 (18759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7699 (t) cc_final: 0.7444 (t) REVERT: A 166 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7073 (ttp80) REVERT: A 500 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7620 (mtt-85) REVERT: B 633 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6467 (mtpt) REVERT: C 137 LYS cc_start: 0.7746 (mttt) cc_final: 0.6690 (pmtt) REVERT: C 347 LYS cc_start: 0.7784 (pttp) cc_final: 0.7465 (pptt) REVERT: C 500 ARG cc_start: 0.7976 (mmt180) cc_final: 0.7684 (mtt-85) REVERT: E 535 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8116 (mmm) REVERT: D 54 CYS cc_start: 0.7587 (t) cc_final: 0.7308 (t) REVERT: D 327 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7597 (mmt180) REVERT: D 500 ARG cc_start: 0.7893 (mmt180) cc_final: 0.7473 (mmt90) REVERT: F 633 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6474 (mtpt) REVERT: F 657 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7248 (tp30) outliers start: 38 outliers final: 18 residues processed: 200 average time/residue: 1.4315 time to fit residues: 310.3448 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 633 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 47 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 157 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN B 591 GLN E 591 GLN D 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124515 restraints weight = 14119.949| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.60 r_work: 0.3253 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13908 Z= 0.130 Angle : 0.595 12.463 18942 Z= 0.299 Chirality : 0.046 0.173 2220 Planarity : 0.004 0.035 2316 Dihedral : 5.248 24.888 2553 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.72 % Allowed : 13.13 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1590 helix: 1.68 (0.27), residues: 417 sheet: 1.02 (0.23), residues: 405 loop : 0.06 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 419 HIS 0.003 0.001 HIS C 105 PHE 0.009 0.001 PHE A 383 TYR 0.010 0.001 TYR A 217 ARG 0.005 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 36) link_NAG-ASN : angle 2.12520 ( 108) link_BETA1-4 : bond 0.00385 ( 3) link_BETA1-4 : angle 1.35983 ( 9) hydrogen bonds : bond 0.04726 ( 459) hydrogen bonds : angle 4.86095 ( 1251) SS BOND : bond 0.00557 ( 33) SS BOND : angle 1.49998 ( 66) covalent geometry : bond 0.00303 (13836) covalent geometry : angle 0.56807 (18759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7437 (t) cc_final: 0.7164 (t) REVERT: A 166 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7106 (ttp80) REVERT: A 500 ARG cc_start: 0.8092 (mmt180) cc_final: 0.7590 (mtt-85) REVERT: B 601 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7518 (mtpm) REVERT: B 633 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6511 (mtpt) REVERT: C 103 GLN cc_start: 0.8346 (mt0) cc_final: 0.7332 (tm-30) REVERT: C 137 LYS cc_start: 0.7778 (mttt) cc_final: 0.6739 (pmtt) REVERT: C 347 LYS cc_start: 0.7692 (pttp) cc_final: 0.7369 (pptt) REVERT: C 500 ARG cc_start: 0.8001 (mmt180) cc_final: 0.7646 (mtt-85) REVERT: E 535 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: D 47 ASP cc_start: 0.8152 (m-30) cc_final: 0.7943 (m-30) REVERT: D 54 CYS cc_start: 0.7371 (t) cc_final: 0.7115 (t) REVERT: D 114 GLN cc_start: 0.7825 (mt0) cc_final: 0.7500 (pt0) REVERT: D 347 LYS cc_start: 0.7638 (pttp) cc_final: 0.7314 (pptt) REVERT: D 500 ARG cc_start: 0.7944 (mmt180) cc_final: 0.7522 (mmt90) REVERT: F 588 ARG cc_start: 0.8223 (ttp-110) cc_final: 0.7850 (ttp80) outliers start: 25 outliers final: 15 residues processed: 184 average time/residue: 1.4082 time to fit residues: 281.3178 Evaluate side-chains 182 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 636 SER Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN E 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.152294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124231 restraints weight = 14216.038| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.60 r_work: 0.3263 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13908 Z= 0.144 Angle : 0.605 12.188 18942 Z= 0.302 Chirality : 0.046 0.182 2220 Planarity : 0.004 0.037 2316 Dihedral : 5.141 23.305 2553 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.58 % Allowed : 13.20 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1590 helix: 1.74 (0.27), residues: 417 sheet: 1.01 (0.22), residues: 426 loop : 0.10 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 419 HIS 0.002 0.001 HIS B 585 PHE 0.011 0.001 PHE C 383 TYR 0.011 0.001 TYR A 217 ARG 0.006 0.000 ARG E 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 36) link_NAG-ASN : angle 2.16127 ( 108) link_BETA1-4 : bond 0.00217 ( 3) link_BETA1-4 : angle 1.54048 ( 9) hydrogen bonds : bond 0.04865 ( 459) hydrogen bonds : angle 4.80514 ( 1251) SS BOND : bond 0.00568 ( 33) SS BOND : angle 1.48074 ( 66) covalent geometry : bond 0.00340 (13836) covalent geometry : angle 0.57779 (18759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11469.42 seconds wall clock time: 196 minutes 14.71 seconds (11774.71 seconds total)